[gmx-users] Error prb

[Marco Ceruso]

Hi
add #inlcude "ions.itp"
right after the DPOSRES_WATER stuff
to your topol.top
then delete 7 waters from the SOL line at end of .top
and then add a line at end of .top wiht the name of your ion and how many.
Marc

-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Tsjerk Wassenaar
Sent: Monday, August 11, 2003 3:45 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Error prb



Dear Sachin,

Since the difference between your top file and the gro file is fourteen 
atoms, I would think it has to do with the adding of the ions. Seven 
waters would have been replaced by seven Cl-, giving a net change of 
fourteen atoms. So are you by chance using the old gro file, without the 
ions, with the modified topology file?

Cheers,

Tsjerk

Xavier Periole wrote:

>
> That is a simple one: the number of atoms defined in your topology
> file (topol.top) is different from the number of atoms that are your
> conf.gro. You have 14 atoms extra in the conf.gro that are not in the
> topology file. Check the missing atoms and include them in the
> topology file.
>
> XAvier
>
>
>
> On Saturday, August 9, 2003, at 02:30  pm, Sachin Gursahani wrote:
>
>> Dear friends....
>>
>> I ve this typical error while i was running the
>> simulation for Cytochrome C...
>>
>> Fatal error: number of coordinates in coordinate file
>> (1HRC_b4pr.gro, 10243)
>>              does not match topology (1HRC.top, 10229)
>> this error occured after i generated the pr.mdp
>> file..and while i was running:
>>
>> grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL}
>> -o ${MOL}_pr
>>
>> please anyone let me know how to solve this one ..
>> .
>> regards
>> Sachin
>>
>> note: ive used the command genion to genion to
>> generate 7 Cl ions coz the total charge on the system
>> is +7 and i wanted to make it 0....
>>
>> the nsteps for mdrun is 150000.
>>
>>
>>
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